HobbyLink JapanHLJ also have a ton of other hobby items, hobby magazines, you name it.

HobbysearchI haven’t bought from them personally, but from what I hear they’re a good site for Zoids (and many other toys).

MandarakeSells items from their shops online and get in a lot of rare things—search on both “Zoids” and “ゾイド”. Be sure to check the item condition before you buy, as they’re sold as-is and opened Zoids are prettymuch at your own risk.

Yahoo!Japan auctions, Zoids categoryTons of items. The one downside? Even if you can understand Japanese, you’ll need a proxy service like Celga, Rinkya, or Shopping Mall Japan to bid for you.

Other Non-US

Hobbylocus (eBay)Another seller I haven’t bought from myself, but other people recommend.

LeoshopI’ve never ordered from Leoshop directly, but I’ve been in on combined orders. Their Zoids stock is sadly dwindling, though they get in some new releases too. Possible warning: I hear that their shipping quotes have been rather odd lately.

Toy-WaveOne of the better-stocked Zoid sources these days, though that’s relative! Besides (occasionally incredible) deals, Ken gets a good amount of obscure and hard to find Zoids stuff in, even if prices may be high for rarities.

YesasiaOften pricy, but occasionally not, and Zoids usually qualify for free shipping. Also has media (CDs, DVDs, etc.)

United States

BigBadToyStoredon’t have many Zoids, but they get in a few new ones on occasion.

Image AnimeThey don’t have a huge Zoid selection any more, but they get some new releases and carry some other modeling supplies.

Jedi Bill's Zoids (eBay)Jedi Bill’s a collector and a reliable seller. Ask him if there’s something you want not listed, he may well have it.

Tatsu HobbyFrom what I hear, Tatsu Hobby are a good place to get the HMM line of Zoids if you’re in the US.